Community structure of the microbiota associated with nodal roots of rice plants along with the growth stages: estimation by PCR-RFLP analysis

Abstract

Community structure of the microbiota in rice roots that developed from different nodes and at different growth stages were compared by using PCR (polymerase chain reaction)-RFLP (restriction fragment length polymorphism) analysis of 16S rDNA. This was the first study to have applied a molecular microbial technique for elucidating the rhizospheric microbial succession of rice roots. Rice plants were grown in submerged soil pots, and nodal roots were collected 5 times during the growing period of rice plants. The RFLP fragments digested by four restriction enzymes (Hinf I, Hae III, Sau3A I, and EcoR I) tended to increase along with the growth stage. A marked increase in the RFLP fragments coincided with the development of reduction in the rhizosphere soil. RFLP fragments that were associated with every nodal root irrespective to the sampling date and those specific to the early and late growth stages were identified. Systematic changes in RFLP patterns from higher (younger) nodal roots to lower (older) nodal roots were also observed at each sampling date, which indicated the succession of the microbial community from higher to lower nodal roots. Cluster analysis divided the RFLP patterns of the microbial community associated with nodal roots into four clusters depending on the growth stages of rice plants. The cluster of the early growth stage was further divided into two subclusters of higher and lower nodal roots. The specific RFLP fragments that contributed to the seasonal variation of the microbial community associated with nodal roots as well as those that characterized the aging of nodal roots were clarified by principal component analysis.